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Volumn 4, Issue 8, 2008, Pages

Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; DISEASES; LIGANDS;

EID: 50949117526     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000138     Document Type: Article
Times cited : (53)

References (56)
  • 1
    • 0031127373 scopus 로고    scopus 로고
    • Human cysteine-rich intestinal protein: CDNA cloning and expression of recombinant protein and identification in human peripheral blood mononuclear cells
    • Khoo C, Blanchard PK, Sullivan VK, Cousins RJ (1997) Human cysteine-rich intestinal protein: cDNA cloning and expression of recombinant protein and identification in human peripheral blood mononuclear cells. Protein Expr Purif 9: 379-387.
    • (1997) Protein Expr Purif , vol.9 , pp. 379-387
    • Khoo, C.1    Blanchard, P.K.2    Sullivan, V.K.3    Cousins, R.J.4
  • 2
    • 0028027427 scopus 로고
    • Isolation and characterization of a cDNA that codes for a LIM-containing protein which is developmentally regulated in heart
    • Tsui SK, Yam NY, Lee CY, Waye MM (1994) Isolation and characterization of a cDNA that codes for a LIM-containing protein which is developmentally regulated in heart. Biochem Biophys Res Commun 205: 497-505.
    • (1994) Biochem Biophys Res Commun , vol.205 , pp. 497-505
    • Tsui, S.K.1    Yam, N.Y.2    Lee, C.Y.3    Waye, M.M.4
  • 4
    • 4344702050 scopus 로고    scopus 로고
    • Thiamine transporter gene expression and exogenous thiamine modulate the expression of genes involved in drug and prostaglandin metabolism in breast cancer cells
    • Liu S, Stromberg A, Tai H, Moscow JA (2004) Thiamine transporter gene expression and exogenous thiamine modulate the expression of genes involved in drug and prostaglandin metabolism in breast cancer cells. Mol Cancer Res 2: 477-487.
    • (2004) Mol Cancer Res , vol.2 , pp. 477-487
    • Liu, S.1    Stromberg, A.2    Tai, H.3    Moscow, J.A.4
  • 5
    • 0037446976 scopus 로고    scopus 로고
    • Identification of cervical cancer markers by cDNA and tissue microarrays
    • Chen Y, Miller C, Mosher R, Zhao X, Deeds J, et al. (2003) Identification of cervical cancer markers by cDNA and tissue microarrays. Cancer Res 63: 1927-1935.
    • (2003) Cancer Res , vol.63 , pp. 1927-1935
    • Chen, Y.1    Miller, C.2    Mosher, R.3    Zhao, X.4    Deeds, J.5
  • 6
    • 19944427466 scopus 로고    scopus 로고
    • Gene expression profiles of primary HPV16- and HPV18-infected early stage cervical cancers and normal cervical epithelium: Identification of novel candidate molecular markers for cervical cancer diagnosis and therapy
    • Santin AD, Zhan F, Bignotti E, Siegel ER, Cane S, et al. (2005) Gene expression profiles of primary HPV16- and HPV18-infected early stage cervical cancers and normal cervical epithelium: identification of novel candidate molecular markers for cervical cancer diagnosis and therapy. Virology 33: 269-291.
    • (2005) Virology , vol.33 , pp. 269-291
    • Santin, A.D.1    Zhan, F.2    Bignotti, E.3    Siegel, E.R.4    Cane, S.5
  • 7
    • 0036098611 scopus 로고    scopus 로고
    • Characterization of gene expression profiles in intraductal papillary-mucinous tumors of the pancreas
    • Terris B, Blaveri E, Crnogorac-Jurcevic T, Jones M, Missiaglia E, et al. (2002) Characterization of gene expression profiles in intraductal papillary-mucinous tumors of the pancreas. Am J Pathol 160: 1745-1754.
    • (2002) Am J Pathol , vol.160 , pp. 1745-1754
    • Terris, B.1    Blaveri, E.2    Crnogorac-Jurcevic, T.3    Jones, M.4    Missiaglia, E.5
  • 8
    • 4544317212 scopus 로고    scopus 로고
    • Analysis of gene expression in cancer cell lines identifies candidate markers for pancreatic tumorigenesis and metastasis
    • Missiaglia E, Blaveri E, Terris B, Wang Y, Costello E, et al. (2004) Analysis of gene expression in cancer cell lines identifies candidate markers for pancreatic tumorigenesis and metastasis. Int J Cancer 112: 100-112.
    • (2004) Int J Cancer , vol.112 , pp. 100-112
    • Missiaglia, E.1    Blaveri, E.2    Terris, B.3    Wang, Y.4    Costello, E.5
  • 9
    • 33748493584 scopus 로고    scopus 로고
    • Transcriptional census of 36 microdissected colorectal cancers yields a gene signature to distinguish UICC II and III
    • Groene J, Mansmann U, Meister R, Staub E, Roepcke S, et al. (2006) Transcriptional census of 36 microdissected colorectal cancers yields a gene signature to distinguish UICC II and III. Int J Cancer 119: 1829-1836.
    • (2006) Int J Cancer , vol.119 , pp. 1829-1836
    • Groene, J.1    Mansmann, U.2    Meister, R.3    Staub, E.4    Roepcke, S.5
  • 11
    • 0141885261 scopus 로고    scopus 로고
    • Combinatorial discovery of tumor targeting peptides using phage display
    • Landon LA, Deutscher SL (2003) Combinatorial discovery of tumor targeting peptides using phage display. J Cell Biochem 90: 509-517.
    • (2003) J Cell Biochem , vol.90 , pp. 509-517
    • Landon, L.A.1    Deutscher, S.L.2
  • 12
    • 9444236174 scopus 로고    scopus 로고
    • Small peptides as potent mimetics of the protein hormone erythropoietin
    • Wrighton NC, Farrell FX, Chang R, Kashyap AK, Barbone FP, et al. (1996) Small peptides as potent mimetics of the protein hormone erythropoietin. Science 273: 458-464.
    • (1996) Science , vol.273 , pp. 458-464
    • Wrighton, N.C.1    Farrell, F.X.2    Chang, R.3    Kashyap, A.K.4    Barbone, F.P.5
  • 13
    • 0032101056 scopus 로고    scopus 로고
    • Characterization of human anti-high molecular weight-melanoma-associated antigen single-chain Fv fragments isolated from a phage display antibody library
    • Desai SA, Wang X, Noronha EJ, Kageshita T, Ferrone S (1998) Characterization of human anti-high molecular weight-melanoma-associated antigen single-chain Fv fragments isolated from a phage display antibody library. Cancer Res 58: 2417-2425.
    • (1998) Cancer Res , vol.58 , pp. 2417-2425
    • Desai, S.A.1    Wang, X.2    Noronha, E.J.3    Kageshita, T.4    Ferrone, S.5
  • 15
    • 10544242963 scopus 로고    scopus 로고
    • A peptide isolated by phage display binds to ICAM-1 and inhibits binding to LFA-1
    • Welply JK, Steininger CN, Caparon M, Michener ML, Howard SC, et al. (1996) A peptide isolated by phage display binds to ICAM-1 and inhibits binding to LFA-1. Proteins 26: 262-270.
    • (1996) Proteins , vol.26 , pp. 262-270
    • Welply, J.K.1    Steininger, C.N.2    Caparon, M.3    Michener, M.L.4    Howard, S.C.5
  • 16
    • 0028831142 scopus 로고
    • Neutralizing recombinant human antibodies to a conformational V2- and CD4-binding site-sensitive epitope of HIV-1 gp120 isolated by using an epitope-masking procedure
    • Ditzel HJ, Binley JM, Moore JP, Sodroski J, Sullivan N, et al. (1995) Neutralizing recombinant human antibodies to a conformational V2- and CD4-binding site-sensitive epitope of HIV-1 gp120 isolated by using an epitope-masking procedure. J Immunol 154: 893-906.
    • (1995) J Immunol , vol.154 , pp. 893-906
    • Ditzel, H.J.1    Binley, J.M.2    Moore, J.P.3    Sodroski, J.4    Sullivan, N.5
  • 18
    • 0029934724 scopus 로고    scopus 로고
    • Identification of a biologically significant DA-binding peptide motif by use of a random phage display library
    • Cheng X, Kay BK, Juliano RL (1996) Identification of a biologically significant DA-binding peptide motif by use of a random phage display library. Gene 171: 1-8.
    • (1996) Gene , vol.171 , pp. 1-8
    • Cheng, X.1    Kay, B.K.2    Juliano, R.L.3
  • 19
    • 0031555904 scopus 로고    scopus 로고
    • Molecular cloning of anti-SS-A/Ro 60-kDa peptide Fab fragments from infiltrating salivary gland lymphocytes of a patient with Sjögren's syndrome
    • Suzuki H, Takemura H, Suzuki M, Sekine Y, Kashiwagi H (1997) Molecular cloning of anti-SS-A/Ro 60-kDa peptide Fab fragments from infiltrating salivary gland lymphocytes of a patient with Sjögren's syndrome. Biochem Biophys Res Commun 232: 101-106.
    • (1997) Biochem Biophys Res Commun , vol.232 , pp. 101-106
    • Suzuki, H.1    Takemura, H.2    Suzuki, M.3    Sekine, Y.4    Kashiwagi, H.5
  • 20
    • 0032518461 scopus 로고    scopus 로고
    • Multidrug-resistance drug-binding peptides generated by using a phage display library
    • Popkov M, Lussier I, Medvedkine V, Esteve PO, Alakhov V, et al. (1998) Multidrug-resistance drug-binding peptides generated by using a phage display library. Eur J Biochem 251: 155-163.
    • (1998) Eur J Biochem , vol.251 , pp. 155-163
    • Popkov, M.1    Lussier, I.2    Medvedkine, V.3    Esteve, P.O.4    Alakhov, V.5
  • 21
    • 23944472220 scopus 로고    scopus 로고
    • Identification of tumor targeting agents by phage display
    • Romanov VI (2005) Identification of tumor targeting agents by phage display. Med Chem Rev 2: 219-229.
    • (2005) Med Chem Rev , vol.2 , pp. 219-229
    • Romanov, V.I.1
  • 22
    • 30744471940 scopus 로고    scopus 로고
    • Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis
    • Hou T, McLaughlin W, Lu B, Chen K, Wang W (2006) Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res 5: 32-43.
    • (2006) J Proteome Res , vol.5 , pp. 32-43
    • Hou, T.1    McLaughlin, W.2    Lu, B.3    Chen, K.4    Wang, W.5
  • 23
    • 0035950043 scopus 로고    scopus 로고
    • Toward the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201
    • Doytchinova IA, Flower DR (2001) Toward the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201. J Med Chem 44: 3572-3581.
    • (2001) J Med Chem , vol.44 , pp. 3572-3581
    • Doytchinova, I.A.1    Flower, D.R.2
  • 24
    • 0031008575 scopus 로고    scopus 로고
    • On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
    • Froloff N, Windemuth A, Honig B (1997) On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions. Protein Sci 6: 1293-1301.
    • (1997) Protein Sci , vol.6 , pp. 1293-1301
    • Froloff, N.1    Windemuth, A.2    Honig, B.3
  • 25
    • 0034789590 scopus 로고    scopus 로고
    • An analysis of the interactions between the Sem-5 SH3 domain and its Ligands using molecular dynamics, free energy calculations, and sequence analysis
    • Wang W, Lim WA, Jakalian A, Wang J, Wang JM, et al. (2001) An analysis of the interactions between the Sem-5 SH3 domain and its Ligands using molecular dynamics, free energy calculations, and sequence analysis. J Am Chem Soc 123: 3986-3994.
    • (2001) J Am Chem Soc , vol.123 , pp. 3986-3994
    • Wang, W.1    Lim, W.A.2    Jakalian, A.3    Wang, J.4    Wang, J.M.5
  • 26
    • 0942266531 scopus 로고    scopus 로고
    • Calculation of affinities of peptides for proteins
    • Donnini S, Juffer AH (2004) Calculation of affinities of peptides for proteins. J Comput Chem 25: 393-411.
    • (2004) J Comput Chem , vol.25 , pp. 393-411
    • Donnini, S.1    Juffer, A.H.2
  • 28
    • 34249777526 scopus 로고    scopus 로고
    • Eris: An automated estimator of protein stability
    • Yin S, Ding F, Dokholyan NV (2007) Eris: An automated estimator of protein stability. Nat Methods 4: 466-467.
    • (2007) Nat Methods , vol.4 , pp. 466-467
    • Yin, S.1    Ding, F.2    Dokholyan, N.V.3
  • 29
    • 36749018607 scopus 로고    scopus 로고
    • Modeling backbone flexibility improves protein stability estimation
    • Yin S, Ding F, Dokholyan NV (2007) Modeling backbone flexibility improves protein stability estimation. Structure 15: 1567-1576.
    • (2007) Structure , vol.15 , pp. 1567-1576
    • Yin, S.1    Ding, F.2    Dokholyan, N.V.3
  • 30
    • 1042298843 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • Kortemme T, Baker D (2004) Computational design of protein-protein interactions. Curr Opin Chem Biol 8: 91-97.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 91-97
    • Kortemme, T.1    Baker, D.2
  • 31
    • 0034724569 scopus 로고    scopus 로고
    • SH3-SPOT: An algorithm to predict preferred ligands to different members of the SH3 gene family
    • Brannetti B, Via A, Cestra G, Cesareni G, Citterich MH (2000) SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J Mol Biol 298: 313-328.
    • (2000) J Mol Biol , vol.298 , pp. 313-328
    • Brannetti, B.1    Via, A.2    Cestra, G.3    Cesareni, G.4    Citterich, M.H.5
  • 32
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy P, Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci U S A 99: 5896-5901.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 33
    • 0035914473 scopus 로고    scopus 로고
    • Virtual interaction profiles of proteins
    • Wollacott AM, Desjarlais JR (2001) Virtual interaction profiles of proteins. J Mol Biol 313: 317-342.
    • (2001) J Mol Biol , vol.313 , pp. 317-342
    • Wollacott, A.M.1    Desjarlais, J.R.2
  • 34
    • 0037447059 scopus 로고    scopus 로고
    • Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases
    • Li L, Shakhnovich EI, Mirny LA (2003) Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A 100: 4463-4468.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 4463-4468
    • Li, L.1    Shakhnovich, E.I.2    Mirny, L.A.3
  • 35
    • 0037422596 scopus 로고    scopus 로고
    • Structural basis and prediction of substrate specificity in protein serine/threonine kinases
    • Brinkworth RI, Breinl RA, Kobe B (2003) Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc Natl Acad Sci U S A 100: 74-79.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 74-79
    • Brinkworth, R.I.1    Breinl, R.A.2    Kobe, B.3
  • 36
    • 0036407643 scopus 로고    scopus 로고
    • Modulating calmodulin binding specificity through computational protein design
    • Shifman JM, Mayo SL (2002) Modulating calmodulin binding specificity through computational protein design. J Mol Biol 323: 417-423.
    • (2002) J Mol Biol , vol.323 , pp. 417-423
    • Shifman, J.M.1    Mayo, S.L.2
  • 38
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • Havranek JJ, Harbury PB (2003) Automated design of specificity in molecular recognition. Nat Struct Mol Biol 10: 45-52.
    • (2003) Nat Struct Mol Biol , vol.10 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 39
    • 50949134076 scopus 로고    scopus 로고
    • Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al. (2001) Analysis of proteins. In: Current Protocols in Molecular Biology. New York: John Wiley & Sons. pp 10.2A.1-10.2A.4.
    • Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al. (2001) Analysis of proteins. In: Current Protocols in Molecular Biology. New York: John Wiley & Sons. pp 10.2A.1-10.2A.4.
  • 40
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
    • (1976) Anal Biochem , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 41
    • 0029633168 scopus 로고
    • Gromacs - a message-passing parallel molecular-dynamics implementation
    • Berendsen HJC, Vanderspoel D, Vandrunen R (1995) Gromacs - a message-passing parallel molecular-dynamics implementation. Comput Phys Commun 91: 43-56.
    • (1995) Comput Phys Commun , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    Vanderspoel, D.2    Vandrunen, R.3
  • 42
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
    • (2001) J Mol Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 44
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118: 11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 46
    • 84986440341 scopus 로고
    • Settle - an analytical version of the shake and rattle algorithm for rigid water models
    • Miyamoto S, Kollman PA (1992) Settle - an analytical version of the shake and rattle algorithm for rigid water models. J Comput Chem 13: 952-962.
    • (1992) J Comput Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 48
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng ZP (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins Struct Funct Genet 52: 80-87.
    • (2003) Proteins Struct Funct Genet , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.P.3
  • 50
    • 1242294472 scopus 로고    scopus 로고
    • Can contact potentials reliably predict stability of proteins?
    • Khatun J, Khare SD, Dokholyan NV (2004) Can contact potentials reliably predict stability of proteins? J Mol Biol 336: 1223-1238.
    • (2004) J Mol Biol , vol.336 , pp. 1223-1238
    • Khatun, J.1    Khare, S.D.2    Dokholyan, N.V.3
  • 51
    • 33746639718 scopus 로고    scopus 로고
    • Emergence of protein fold families through rational design
    • doi:10.1371/journal.pcbi.0020085
    • Ding F, Dokholyan NV (2006) Emergence of protein fold families through rational design. PLoS Comput Biol 2: e85. doi:10.1371/journal.pcbi.0020085.
    • (2006) PLoS Comput Biol , vol.2
    • Ding, F.1    Dokholyan, N.V.2
  • 52
    • 0033231449 scopus 로고    scopus 로고
    • Simultaneous assay of Src SH3 and SH2 domain binding using different wavelength fluorescence polarization probes
    • Lynch BA, Minor C, Loiacono KA, van Schravendijk MR, Ram MK, et al. (1999) Simultaneous assay of Src SH3 and SH2 domain binding using different wavelength fluorescence polarization probes. Anal Biochem 275: 62-73.
    • (1999) Anal Biochem , vol.275 , pp. 62-73
    • Lynch, B.A.1    Minor, C.2    Loiacono, K.A.3    van Schravendijk, M.R.4    Ram, M.K.5
  • 53
    • 4444323608 scopus 로고    scopus 로고
    • A novel approach to the regioselective synthesis of a disulfide-linked heterodimeric bicyclic peptide mimetic of brain-derived neurotrophic factor
    • Fletcher JM, Hughes RA (2004) A novel approach to the regioselective synthesis of a disulfide-linked heterodimeric bicyclic peptide mimetic of brain-derived neurotrophic factor. Tetrahedron Lett 45: 6999-7001.
    • (2004) Tetrahedron Lett , vol.45 , pp. 6999-7001
    • Fletcher, J.M.1    Hughes, R.A.2
  • 54
    • 50949114884 scopus 로고    scopus 로고
    • Fitting Models to Biological Data Using Linear and Nonlinear Regression
    • Motulsky H, Christopoulos A (2005) Fitting Models to Biological Data Using Linear and Nonlinear Regression. San Diego (California): GraphPad. pp 199-210.
    • (2005) San Diego (California): GraphPad , pp. 199-210
    • Motulsky, H.1    Christopoulos, A.2
  • 55
    • 33847677302 scopus 로고    scopus 로고
    • Dibenzothiazole as novel amyloid-imaging agents
    • Wu C, Wei J, Gao K, Wang Y (2007) Dibenzothiazole as novel amyloid-imaging agents. Bioorg Med Chem 12: 2789-2796.
    • (2007) Bioorg Med Chem , vol.12 , pp. 2789-2796
    • Wu, C.1    Wei, J.2    Gao, K.3    Wang, Y.4


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